PMID:17900620

Citation	Summer, EJ, Berry, J, Tran, TA, Niu, L, Struck, DK and Young, R (2007) Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts. J. Mol. Biol. 373:1098-112
Abstract	Under usual laboratory conditions, lysis by bacteriophage lambda requires only the holin and endolysin genes, but not the Rz and Rz1 genes, of the lysis cassette. Defects in Rz or Rz1 block lysis only in the presence of high concentrations of divalent cations. The lambda Rz and Rz1 lysis genes are remarkable in that Rz1, encoding an outer membrane lipoprotein, is completely embedded in the +1 register within Rz, which itself encodes an integral inner membrane protein. While Rz and Rz1 equivalents have been identified in T7 and P2, most phages, including such well-studied classic phages as T4, P1, T1, Mu and SP6, lack annotated Rz/Rz1 equivalents. Here we report that a search strategy based primarily on gene arrangement and membrane localization signals rather than sequence similarity has revealed that Rz/Rz1 equivalents are nearly ubiquitous among phages of Gram-negative hosts, with 120 of 137 phages possessing genes that fit the search criteria. In the case of T4, a deletion of a non-overlapping gene pair pseT.2 and pseT.3 identified as Rz/Rz1 equivalents resulted in the same divalent cation-dependent lysis phenotype. Remarkably, in T1 and six other phages, Rz/Rz1 pairs were not found but a single gene encoding an outer membrane lipoprotein with a C-terminal transmembrane domain capable of integration into the inner membrane was identified. These proteins were named "spanins," since their protein products are predicted to span the periplasm providing a physical connection between the inner and outer membranes. The T1 spanin gene was shown to complement the lambda Rz-Rz1- lysis defect, indicating that spanins function as Rz/Rz1 equivalents. The widespread presence of Rz/Rz1 or their spanin equivalents in phages of Gram-negative hosts suggests a strong selective advantage and that their role in the ecology of these phages is greater than that inferred from the mild laboratory phenotype.
Links	PubMed Online version:10.1016/j.jmb.2007.08.045
Keywords	Bacteriophages/genetics; Gene Rearrangement; Gram-Negative Bacteria/virology; Membrane Proteins; Mutation; Phenotype; Viral Proteins/genetics
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
BPT1:SPANU		GO:0044659: cytolysis by virus of host cell		UniProtKB:P00726 UniProtKB:Q37935	P		Figure 4. shows the function of T1 gp11 restore the function of lambda Rz and Rz1.	Missing: evidence CACAO 10373
BPT1:SPANU		GO:0045203: integral component of cell outer membrane		UniProtKB:Q37935	C		The T1 gp11 was found to have a sequence that very likely predicts an outer membrane lipoprotein, just as Lambda Rz1 produces an outer membrane lipoprotein component of a spanin (p. 1098). In addition, many phages, including Lambda, have a lysis cassette, which means that the holin, endolysin, and spanin are all next to each other in the genome (p. 1100). In the case of T1, genes 12 and 13 are the endolysin and holin, respectively, providing further evidence that gp11 is an integral component of the cell outer membrane. (I've also requested a new GO term to use for gp11, since this paper indicates that the protein disrupts the outer membrane. The issue can be found here https://github.com/geneontology/go-ontology/issues/12424).	Missing: evidence CACAO 11890
BPT1:SPANU		GO:0045203: integral component of cell outer membrane	ECO:0000317: genomic context evidence used in manual assertion	UniProtKB:Q37935	C		The T1 gp11 was found to have a sequence that very likely predicts an outer membrane lipoprotein, just as Lambda Rz1 produces an outer membrane lipoprotein component of a spanin (p. 1098). In addition, many phages, including Lambda, have a lysis cassette, which means that the holin, endolysin, and spanin are all next to each other in the genome (p. 1100). In the case of T1, genes 12 and 13 are the endolysin and holin, respectively, providing further evidence that gp11 is an integral component of the cell outer membrane. (I've also requested a new GO term to use for gp11, since this paper indicates that the protein disrupts the outer membrane. The issue can be found here https://github.com/geneontology/go-ontology/issues/12424).	complete
BPT1:SPANU		GO:0090680: disruption by virus of host outer membrane	ECO:0000317: genomic context evidence used in manual assertion		P			Missing: with/from
BPT4:SPAN1		GO:0044659: cytolysis by virus of host cell	ECO:0000316:	UniProtKB:P39503	P		Figure 2. Shows pseT.3 (spanin outter subunit) facilitates cytolysis. A graph shows the OD of cultures at different timepoints, with infections of different T4 genotypes, and clearly demonstrates pseT.3 facilitates cytolysis of the host cell.	complete CACAO 10359
BPT4:SPAN1	involved_in	GO:0044659: cytolysis by virus of host cell	ECO:0000316: genetic interaction evidence used in manual assertion	UniProtKB:P39503	P		Seeded From UniProt	complete
BPT4:SPAN2		GO:0044659: cytolysis by virus of host cell	ECO:0000316:	UniProtKB:P39504	P		Figure 2. Shows pseT.2 (spanin outter subunit) facilitates cytolysis. A graph shows the OD of cultures at different timepoints, with infections of different T4 genotypes, and clearly demonstrates pseT.2 facilitates cytolysis of the host cell.	complete CACAO 10360
BPT4:SPAN2	involved_in	GO:0044659: cytolysis by virus of host cell	ECO:0000316: genetic interaction evidence used in manual assertion	UniProtKB:P39504	P		Seeded From UniProt	complete

References

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